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comparison galaxy-conf/DynaPro.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
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children 3e477c7e0e73
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11:b1952a90d4bf 12:81d5b81fb3c2
1 <tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.0.0">
2 <description>using DynaPro</description>
3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N
4 #if str( $mean ) != ''
5 -m $mean
6 #end if
7
8 #if str( $variance ) != ''
9 -v $variance
10 #end if
11 -o $output
12 </command>
13 <inputs>
14 <param format="bigwig,wig" name="input" type="data" label="Energy landscape" />
15 <param name="N" type="integer" value="147" label="Nucleosome size (bp)" />
16 <param name="mean" type="float" optional="true" label="Shift energy landscape to have mean" />
17 <param name="variance" type="float" optional="true" label="Rescale energy landscape to have variance" />
18 </inputs>
19 <outputs>
20 <data format="wig" name="output" metadata_source="input" />
21 </outputs>
22 <help>
23
24 .. class:: warningmark
25
26 At present, this tool is only suitable for small genomes (yeast) since entire chromosomes must be loaded into memory.
27
28 -----
29
30 Equilibrium nucleosome distribution is modeled as a one-dimensional fluid of hard rods adsorbing and moving within an external potential. This tool provides a simplified version of the DynaPro_ algorithm for a single factor interacting with hard-core repulsion.
31
32 .. _DynaPro: http://nucleosome.rutgers.edu/nucleosome/
33
34 -----
35
36 **Syntax**
37
38 - **Energy landscape** is the external potential function for each genomic base pair, and must be in Wig format.
39 - **Nucleosome size** is the hard-core interaction size.
40
41 -----
42
43 **Citation**
44
45 Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J and Siggia ED (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37: 4707–4722.
46
47 </help>
48 </tool>